Since your a self proclaimed newbie, let me first start off by saying that a pork shoulder does not necessarily take 12 hours. It might, but then again it might not. It depends on many variables. Always cook to the desired internal meat tempature and not by the amount of time you assume it's going to take.
The meat will continue to take on smoke flavor throughout the cooking process no matter when add the wood. Unless you plan on foiling when the meat hits a certain tempature. Then obviously the meat is wrapped in foil and is just braising in it's own juices + whatever other liquid you may have added. But you do not have to foil. Many do since it creates a moist environment and the meat just becomes fall apart tender.
If you have not been through the 5-day ecourse, I recommend doing that.
is a link to Jeff's on-line recipie for doing a shoulder.
I would recommend that you start with smoke right from the get-go. Then you can go nap for a few hours (if you're convinced the smoker will be safe and hold temps without supervision) and come back and probe the meat with a quality, calibrated thermometer. When the meat hits 165*F internal temp, wrap in some heavy duty alluminum foil. Add in some apple juice, beer, water, some sort of liquid to help the braising. Then you can go back and nap for a couple more hours. When the meat hits 200-205* pull it from the smoker, and let it rest in a dry cooler wrapped in towels for and hour or two. It'll stay piping hot this way and the meat will continue to break down. Then just open 'er up and start pulling.
Oh, and don't forget the qview. Good luck